uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis
Class BlastOverlapAnalysis

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
      extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
          extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
              extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BlastOverlapAnalysis
All Implemented Interfaces:
BasicFeatureAnalysisAble

public class BlastOverlapAnalysis
extends FeatureOverlapAnalysis

Analysis class which calculates the high scoring path in a clustered sequence using the Blast overlap on the exon level

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
BlastOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfBlastRegions, SimpleArg _allArguments)
          constructor for BlastOverlapAnalysis objects
 
Method Summary
 java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          method which returns the high scoring path of genemodels on a sequence using the Blast overlap on the exon level.
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
getArrListOfFeatRegions
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
getAllArguments, getArrListOfGMRegions, getClassName
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BlastOverlapAnalysis

public BlastOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions,
                            java.util.ArrayList _arrListOfBlastRegions,
                            SimpleArg _allArguments)
constructor for BlastOverlapAnalysis objects

Parameters:
_arrListOfGMRegions - ArrayList of genemodel regions
_arrListOfBlastRegions - ArrayList of blast regions
_allArguments - SimpleArg object which contains all command line arguments
See Also:
GeneModel, SimFeature, GFMergeRegion
Method Detail

getHighScoringGmRegArr

public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
method which returns the high scoring path of genemodels on a sequence using the Blast overlap on the exon level.

Blast hits from the same protein to a genemodel are treated as one hit. Longest protein hit is chosen for scoring the genemodel. For further details consult the documentation.

Specified by:
getHighScoringGmRegArr in interface BasicFeatureAnalysisAble
Specified by:
getHighScoringGmRegArr in class BasicFeatureAnalysis
Parameters:
_arrListOfGMRegionsToAnalyze - ArrayList of genemodel regions
Returns:
ArrayList of regions with high scoring genemodels